- d -

• D : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• d2h_sa_reweight : basic::options::OptionKeys::in::file
• D_alpha_comp_file : basic::options::OptionKeys::cyclic_peptide
• D_beta_comp_file : basic::options::OptionKeys::cyclic_peptide
• D_inv_sqr : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• d_max : basic::options::OptionKeys::score::saxs
• d_min : basic::options::OptionKeys::score::saxs
• d_step : basic::options::OptionKeys::score::saxs
• da_eval_pose_map : basic::options::OptionKeys::DomainAssembly
• da_linker_file : basic::options::OptionKeys::DomainAssembly
• da_linker_file_rna : basic::options::OptionKeys::DomainAssembly
• da_nruns : basic::options::OptionKeys::DomainAssembly
• da_require_buried : basic::options::OptionKeys::DomainAssembly
• da_setup : basic::options::OptionKeys::DomainAssembly
• da_setup_option_file : basic::options::OptionKeys::DomainAssembly
• da_setup_output_pdb : basic::options::OptionKeys::DomainAssembly
• da_start_pdb : basic::options::OptionKeys::DomainAssembly
• da_start_pdb_num : basic::options::OptionKeys::DomainAssembly
• dalphaball : basic::options::OptionKeys::holes
• dang : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• darc_components : basic::options::OptionKeys::fingerprint
• darc_elsts_only : basic::options::OptionKeys::fingerprint
• darc_shape_only : basic::options::OptionKeys::fingerprint
• dat : hist2d
• data : 3d_histogram , add_xyz_to_pose , erraser_single_res_analysis , get_junctions_from_legos , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , plot , solution_counts , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• data_file : basic::options::OptionKeys::motifs , basic::options::OptionKeys::rna
• data_in : basic::options::OptionKeys::optE
• data_out : basic::options::OptionKeys::optE
• database : basic::options::OptionKeys::in::path , kic_runner
• database_cache_dir : basic::options::OptionKeys::in::path
• database_filter : basic::options::OptionKeys::out
• database_name : basic::options::OptionKeys::inout::dbms
• database_partition : basic::options::OptionKeys::inout::dbms
• database_protocol_id : basic::options::OptionKeys::out
• datefmt : pyrosetta.tests.distributed.test_dask
• datr : test_mm_lj
• datr1 : test_mm_lj
• datr2 : test_mm_lj
• dats : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• db : basic::options::OptionKeys::out::path , basic::options::OptionKeys::rna::denovo::db
• db_path : basic::options::OptionKeys::lh
• dbms : basic::options::OptionKeys::in::dbms , basic::options::OptionKeys::inout::dbms
• dc : basic::options::OptionKeys::dc , basic::options::OptionKeys::in::file
• dd_parser : basic::options::OptionKeys::jd2
• ddg : basic::options::OptionKeys::ddg
• ddg_cutoff : basic::options::OptionKeys::motifs
• DDG_cutoff : protocols::pmut_scan
• ddg_cycles : revert_app
• ddg_predictions_file : basic::options::OptionKeys::in::file
• ddih : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• ddis : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• debug : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys , basic::options::OptionKeys::edensity , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::holes , basic::options::OptionKeys::james , basic::options::OptionKeys::loodo , basic::options::OptionKeys::loops , basic::options::OptionKeys::membrane , basic::options::OptionKeys::msd , basic::options::OptionKeys::run , basic::options::OptionKeys::smhybrid
• DEBUG : PyMOL-Rosetta-relay-client
• debug_derivatives : basic::options::OptionKeys::edensity
• debug_inaccurate_G : basic::options::OptionKeys::optimization
• debug_loop_closure : basic::options::OptionKeys::loops
• debug_output : basic::options::OptionKeys::ddg
• debug_skip_fragment_generation : basic::options::OptionKeys
• debug_structures : basic::options::OptionKeys::abinitio
• decoystats : basic::options::OptionKeys::run
• default : 3d_histogram , app_runner , auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , autocorrelation , closure_error , correlation_time , demo.D010_Pose_structure , demo.D020_Pose_scoring , demo.D030_Fold_tree , demo.D040_Movemap , demo.D050_Packer_task , demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D090_Ala_scan , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface , DRRAFTER , drrafter_rna , dummy-distribution , enumerate_junctions , execute , explosion_error , find_lowest_scoring_relaxed_struct , gaussian-sampling , general_RNP_setup_script , get_final_ddG_scores , get_lowest_scoring_relaxed_models , histogram , job_manager , kic_runner , options_will , percent_subangstrom , pivot_selection , plot , pyrosetta.tests.distributed.cluster.print_discovered_test_cases , relax_starting_structure , run_backbone , run_sidechain , score_vs_rmsd , setup_for_complex_scoring_general , submit_jobs
• default_algorithm : kic_runner
• default_breadth_move : run_backbone
• default_buffer_size : utility::io::mpi_stream , zlib_stream
• default_closure_move : run_backbone
• default_color : test.T150_PyMOL_Integration
• DEFAULT_DEPRECATION_MESSAGE : ez_setup
• default_max_cycles : basic::options::OptionKeys::optimization
• default_movement_params : basic::options::OptionKeys::RBSegmentRelax
• default_name : execute , kic_runner , run_backbone , run_sidechain
• default_pivots : run_backbone
• default_rama_sampling_table : basic::options::OptionKeys::cyclic_peptide
• default_repeats : basic::options::OptionKeys::relax
• default_residues : execute , run_sidechain
• default_sampling_move : run_backbone
• DEFAULT_SAVE_DIR : ez_setup
• default_score_function : run_backbone
• default_structure : execute , kic_runner , run_backbone , run_sidechain
• DEFAULT_URL : ez_setup
• DEFAULT_VERSION : ez_setup
• define_match_by_single_downstream_positioning : basic::options::OptionKeys::match
• definitely_virtualize : basic::options::OptionKeys::stepwise
• deg2rad : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• degrees_to_radians : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• delay : basic::options::OptionKeys::run
• delete_checkpoints : basic::options::OptionKeys::run
• delete_interface_native_sidechains : basic::options::OptionKeys::AnchoredDesign::testing
• delete_old_poses : basic::options::OptionKeys::jd2
• delphi_grid : basic::options::OptionKeys::fingerprint
• delta1 : erraser_analysis
• delta2 : erraser_analysis
• deltaE : test.Workshop4test
• denied_pdb : basic::options::OptionKeys::frags
• denom : predPRE
• denominator : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• denovo : basic::options::OptionKeys::rna::denovo
• DenovoProteinDesign : basic::options::OptionKeys::DenovoProteinDesign
• dens_thr : drrafter_rna
• density : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::sc , score_vs_rmsd
• depc_ms_input : basic::options::OptionKeys::score
• depth : basic::options::OptionKeys::frags
• deriv_check : basic::options::OptionKeys::rna::denovo::minimize
• derive_torsion_string_from_native_pose : basic::options::OptionKeys::loops
• desc : options_will
• describe_fragments : basic::options::OptionKeys::frags
• description_file : basic::options::OptionKeys::boinc
• design : basic::options::OptionKeys::antibody::design , basic::options::OptionKeys::dna::design , basic::options::OptionKeys::matdes::design , basic::options::OptionKeys::remodel::design , basic::options::OptionKeys::rot_anl , basic::options::OptionKeys::smhybrid , revert_app
• design_all : basic::options::OptionKeys::remodel::design
• design_antigen : basic::options::OptionKeys::antibody::design
• design_around_ligand : basic::options::OptionKeys::remodel
• design_chains : basic::options::OptionKeys::docking
• design_contrast : basic::options::OptionKeys::out::file
• design_DNA : basic::options::OptionKeys::dna::specificity
• design_first : basic::options::OptionKeys::optE
• design_framework : basic::options::OptionKeys::antibody::design
• design_H3_stem : basic::options::OptionKeys::antibody::design
• design_hydrophobic : basic::options::OptionKeys::smhybrid
• design_interface : basic::options::OptionKeys::willmatch
• design_linker : basic::options::OptionKeys::smhybrid
• design_loop_num : hbs_design , oop_design , peptoid_design
• design_min_cycles : basic::options::OptionKeys::enzdes
• design_neighbors : basic::options::OptionKeys::remodel::design
• design_peptide : basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::flexPepDocking
• design_proline : basic::options::OptionKeys::antibody::design
• design_protocol : basic::options::OptionKeys::antibody::design
• design_radius : chrisk
• design_res_files : basic::options::OptionKeys::smhybrid
• design_rounds : basic::options::OptionKeys::msd
• design_with_fast_design : basic::options::OptionKeys::optE
• design_with_minpack : basic::options::OptionKeys::optE
• design_with_offrotpack : basic::options::OptionKeys::optE
• designable_second_shell : basic::options::OptionKeys::dna::design
• designing_with_noncanonicals : basic::options::OptionKeys::stepwise::monte_carlo
• designs_rd1 : enumerate_junctions
• designs_rd2 : enumerate_junctions
• desn_mc_temp : a3b_hddm , dddm , oddm , tddm
• desn_ta_min : create_a3b_hbs
• dest : demo.D010_Pose_structure , demo.D020_Pose_scoring , demo.D030_Fold_tree , demo.D040_Movemap , demo.D050_Packer_task , demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D090_Ala_scan , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface , execute , kic_runner , run_backbone , run_sidechain , setup_for_complex_scoring_general , solution_counts
• detect_bonds : basic::options::OptionKeys::symmetry
• detect_design_interface : basic::options::OptionKeys::enzdes
• detect_disulf : basic::options::OptionKeys::in
• detect_disulf_tolerance : basic::options::OptionKeys::in
• detect_disulfide_before_relax : basic::options::OptionKeys::abinitio
• detect_oops : basic::options::OptionKeys::in
• devel_apps : config
• device : basic::options::OptionKeys::gpu
• dharm : vancomycin
• dharm2 : vancomycin
• dharm3 : vancomycin
• dhr_location : enumerate_junctions
• DHR_location_digs : enumerate_junctions
• DHR_location_hyak : enumerate_junctions
• DHR_location_jojo : enumerate_junctions
• DHR_location_short : enumerate_junctions
• dhr_run_location : enumerate_junctions
• dhrs_dict : enumerate_junctions
• dialog : PyMOL-Rosetta-relay-client
• diff : erraser_analysis
• differences : compute_difference
• dih : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dih_lst : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dih_mat : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dihedral_cst_weight : basic::options::OptionKeys::antibody::design , local
• dihedral_max : ss_finder
• dihedral_min : ss_finder
• dihedral_pattern : ss_finder
• dihval : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• direction : build_jacobian
• directory : closure_error , explosion_error
• dis : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dis_lst : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dis_mat : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• disable_all_filters : basic::options::OptionKeys::filters
• disable_co_filter : basic::options::OptionKeys::filters
• disable_orientation_dependent_rna_ch_o_bonds : basic::options::OptionKeys::score::rna
• disable_rg_filter : basic::options::OptionKeys::filters
• disable_sampling_of_loop_takeoff : basic::options::OptionKeys::stepwise::protein
• disable_sheet_filter : basic::options::OptionKeys::filters
• disallow_aa : basic::options::OptionKeys::antibody::design
• disallow_bps_at_extra_min_res : basic::options::OptionKeys::rna::denovo
• disallow_pack_polar_hydrogens : basic::options::OptionKeys::stepwise::polar_hydrogens
• disallow_vary_geometry_proton_chi : basic::options::OptionKeys::stepwise::polar_hydrogens
• display_water_hb_network : basic::options::OptionKeys::hydrate
• disregard_num_segment_matches : basic::options::OptionKeys::legacy_sewing
• dissimilarity : ss_finder
• dist : add_xyz_to_pose , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , lactamize , ncontact , plot_hb , predPRE
• dist_cst_weight : local
• dist_cut_off : basic::options::OptionKeys::fingerprint
• dist_cutoff : basic::options::OptionKeys::bunsat_calc2 , basic::options::OptionKeys::mp::lipid_acc
• dist_cutoffs : basic::options::OptionKeys::frags::contacts
• dist_thresholds : basic::options::OptionKeys::james
• distance : build_jacobian
• distance_constraint_prob_cutoff : basic::options::OptionKeys::trRosetta
• distance_constraint_weight : basic::options::OptionKeys::trRosetta
• distance_cutoff : basic::options::OptionKeys::contactMap
• distance_matrix : basic::options::OptionKeys::contactMap
• distance_sampling : basic::options::OptionKeys
• distance_tolerance : basic::options::OptionKeys::loodo
• distinguish_pucker : basic::options::OptionKeys::stepwise::rna
• distributed_cluster_test_cases : test.T900_distributed
• distributed_test_suites : test.T900_distributed
• disulf_cutoff_postrelax : basic::options::OptionKeys::cyclic_peptide
• disulf_cutoff_prerelax : basic::options::OptionKeys::cyclic_peptide
• disulf_landing_range : basic::options::OptionKeys::remodel
• disulf_matching_probe : basic::options::OptionKeys::score
• disulfide_file : basic::options::OptionKeys::stepwise::protein
• disulfide_positions : basic::options::OptionKeys::cluster::energy_based_clustering
• disulfide_res : basic::options::OptionKeys::full_model
• disulfide_scorer : basic::options::OptionKeys::blivens::disulfide_scorer
• DisulfideInsertion : basic::options::OptionKeys::DisulfideInsertion
• diversify_lvl : basic::options::OptionKeys::pepspec
• diversify_pep_seqs : basic::options::OptionKeys::pepspec
• dleu : vancomycin
• dleu_type : vancomycin
• DMS_careful_base_pair_classifier : basic::options::OptionKeys::score::rna
• DMS_separate_features : basic::options::OptionKeys::score::rna
• dna : basic::options::OptionKeys::dna
• dna_backbone_torsion_sdevs : basic::options::OptionKeys::dna::specificity
• dna_chi_torsion_sdev : basic::options::OptionKeys::dna::specificity
• dna_defs : basic::options::OptionKeys::dna::design
• dna_defs_file : basic::options::OptionKeys::dna::design
• dna_move : basic::options::OptionKeys::relax
• dna_p : test.T880_Other
• dna_sugar_torsion_sdev : basic::options::OptionKeys::dna::specificity
• do_dock : basic::options::OptionKeys::antibody::design
• do_final_fullatom_refinement : basic::options::OptionKeys::helical_bundle_predict
• do_final_repack : basic::options::OptionKeys::relax::centroid
• do_minimization : basic::options::OptionKeys::make_mainchain_potential
• do_minimize : basic::options::OptionKeys::peptide_deriver
• do_not_archive_on_node0 : basic::options::OptionKeys::jd3
• do_not_autoassign_SS : basic::options::OptionKeys::out::file
• do_not_count_adjacent_res_hbonds : basic::options::OptionKeys::cyclic_peptide
• do_not_recalc_convergence : drrafter_rna
• do_not_remove_connection_inconsistencies : basic::options::OptionKeys::legacy_sewing
• do_not_sample_multiple_virtual_sugar : basic::options::OptionKeys::stepwise::rna
• dock : basic::options::OptionKeys::matdes::dock , basic::options::OptionKeys::mp::dock
• dock_chunks : basic::options::OptionKeys::rna::denovo
• dock_cycle_rounds : basic::options::OptionKeys::antibody::design
• dock_design_loop_num : a3b_hddm , oddm , tddm
• dock_each_chunk : basic::options::OptionKeys::rna::denovo
• dock_each_chunk_per_chain : basic::options::OptionKeys::rna::denovo
• dock_first_cycles : basic::options::OptionKeys::antibody::design
• dock_hires : test.Workshop7test
• dock_into_density : basic::options::OptionKeys::rna::denovo
• dock_into_density_legacy : basic::options::OptionKeys::rna::denovo
• dock_jump : docking , test.T600_Docking
• dock_lowres : test.Workshop7test
• dock_lowres_filter : basic::options::OptionKeys::docking
• dock_mcm_first_cycles : basic::options::OptionKeys::docking
• dock_mcm_rot_magnitude : basic::options::OptionKeys::docking
• dock_mcm_second_cycles : basic::options::OptionKeys::docking
• dock_mcm_trans_magnitude : basic::options::OptionKeys::docking
• dock_min : basic::options::OptionKeys::docking
• dock_p : test.T600_Docking
• dock_pert : basic::options::OptionKeys::docking , docking , test.T600_Docking
• dock_ppk : basic::options::OptionKeys::docking
• dock_prot : docking
• dock_rtmin : basic::options::OptionKeys::docking
• dock_second_cycles : basic::options::OptionKeys::antibody::design
• dock_trials : basic::options::OptionKeys::enzdes
• docking : basic::options::OptionKeys::docking
• docking_centroid_inner_cycles : basic::options::OptionKeys::docking
• docking_centroid_outer_cycles : basic::options::OptionKeys::docking
• docking_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• docking_highres : docking
• docking_interface_score : basic::options::OptionKeys::score
• docking_jump : docking
• docking_local_refine : basic::options::OptionKeys::docking
• docking_low_res_score : basic::options::OptionKeys::docking
• docking_lowres : docking , test.T600_Docking
• docking_move_size : basic::options::OptionKeys::rna::denovo
• docklowres_rot_magnitude : basic::options::OptionKeys::docking
• docklowres_trans_magnitude : basic::options::OptionKeys::docking
• DockMetrics : basic::options::OptionKeys::evaluation
• domain_map : benchmark_ns
• domain_residue_list : benchmark_ns
• DomainAssembly : basic::options::OptionKeys::DomainAssembly
• domainFusion : basic::options::OptionKeys::remodel::domainFusion
• done : gpu_set_args
• dont_hydrate_hb_engaged_bb_O : basic::options::OptionKeys::hydrate
• dont_minimize_omega : basic::options::OptionKeys::chemically_conjugated_docking
• dont_mutate_correct_charge : local
• dont_mutate_glyprocys : local
• dont_mutate_hbonded_sidechains : local
• dont_rewrite_dunbrack_database : basic::options::OptionKeys::out::file
• dont_use_reference_energies : basic::options::OptionKeys::optE
• dont_use_symm_in_pcalc : basic::options::OptionKeys::patterson
• double_lazy_ig : basic::options::OptionKeys::packing
• double_mutant_scan : protocols::pmut_scan
• double_vesicle_distance : basic::options::OptionKeys::mp::geo
• double_vesicle_inner_radius : basic::options::OptionKeys::mp::geo
• dphis : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dpi : bin_torsions , closure_error , explosion_error , subloop_histogram
• dpsis : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• dr_cycles : basic::options::OptionKeys::remodel , basic::options::OptionKeys::ufv
• draw : kmeans_adaptive_kernel_density_bb_dependent_rotlib , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• drep : test_mm_lj
• drep1 : test_mm_lj
• drep2 : test_mm_lj
• dry_run : basic::options::OptionKeys::out , basic::options::OptionKeys::run , execute , run_backbone , run_sidechain
• dscore_cutoff : basic::options::OptionKeys::dna::design::reversion
• dspec_cutoff : basic::options::OptionKeys::dna::design::reversion
• dssp : basic::options::OptionKeys::in::file
• dssp1 : basic::options::OptionKeys::mh::filter
• dssp2 : basic::options::OptionKeys::mh::filter
• dt : test.T900_distributed
• dtest : basic::options::OptionKeys::motifs
• dualspace : basic::options::OptionKeys::relax
• dump : basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::mh::dump , basic::options::OptionKeys::mh::harvest , basic::options::OptionKeys::rna::denovo::out , basic::options::OptionKeys::stepwise
• dump_all_As : basic::options::OptionKeys::loodo
• dump_all_Bs : basic::options::OptionKeys::loodo
• dump_cg_bb : basic::options::OptionKeys::pepspec
• dump_chainA_only : basic::options::OptionKeys::matdes::dock
• dump_connollySurface : basic::options::OptionKeys::pocket_grid
• dump_coord_cst_weight_array : basic::options::OptionKeys::loopfcst
• dump_cst_set : basic::options::OptionKeys::constraints
• dump_cyclic_poses : basic::options::OptionKeys::peptide_deriver
• dump_espGrid : basic::options::OptionKeys::pocket_grid
• dump_every_model : basic::options::OptionKeys::legacy_sewing
• dump_final_repack_without_ligand_pdb : basic::options::OptionKeys::enzdes
• dump_frags : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::jumps
• dump_freq : basic::options::OptionKeys::recces
• dump_Grid : basic::options::OptionKeys::pocket_grid
• dump_initial_results : indel
• dump_input_pdb : basic::options::OptionKeys::mh
• dump_inverse_rotamers : basic::options::OptionKeys::enzdes
• dump_loop_samples : basic::options::OptionKeys::enzdes
• dump_loops_only : basic::options::OptionKeys::canonical_sampling::sampling
• dump_matching_motifs : basic::options::OptionKeys::mh
• dump_motif_pdbs : basic::options::OptionKeys::mh
• dump_motifs : basic::options::OptionKeys::motifs
• dump_pdb : basic::options::OptionKeys::matdes::dock , basic::options::OptionKeys::recces , basic::options::OptionKeys::rot_anl
• dump_pdbs : basic::options::OptionKeys::ddg , basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::legacy_sewing
• dump_peptide_pdb : peptide_deriver
• dump_peptide_pose : basic::options::OptionKeys::peptide_deriver
• dump_pocketGrid : basic::options::OptionKeys::pocket_grid
• dump_prepared_pose : basic::options::OptionKeys::peptide_deriver
• dump_report_file : basic::options::OptionKeys::peptide_deriver
• dump_rotamer_sets : basic::options::OptionKeys::packing
• dump_rotamers : basic::options::OptionKeys::ralford::dump_rotamers
• dump_silent : basic::options::OptionKeys::recces
• dump_stems : basic::options::OptionKeys::rna::denovo
• dump_templates : basic::options::OptionKeys::tcrmodel
• dump_threshold : ss_finder
• dump_trajectory : basic::options::OptionKeys::dump_trajectory
• dump_transfac : basic::options::OptionKeys::mean_field
• dump_weight_trajectory : basic::options::OptionKeys::rdc
• dumpPDB_abinitio : basic::options::OptionKeys::flexPepDocking
• dumpPDB_hires : basic::options::OptionKeys::flexPepDocking
• dumpPDB_lowres : basic::options::OptionKeys::flexPepDocking
• dun02_file : basic::options::OptionKeys::corrections::score
• dun10 : basic::options::OptionKeys::corrections::score
• dun10_dir : basic::options::OptionKeys::corrections::score
• dun_entropy_correction : basic::options::OptionKeys::corrections::score
• dun_normsd : basic::options::OptionKeys::corrections::score
• dunbrack_prob_buried : basic::options::OptionKeys::packing
• dunbrack_prob_buried_semi : basic::options::OptionKeys::packing
• dunbrack_prob_nonburied : basic::options::OptionKeys::packing
• dunbrack_prob_nonburied_semi : basic::options::OptionKeys::packing
• duplicate_angle_cutoff : basic::options::OptionKeys::motifs
• duplicate_dist_cutoff : basic::options::OptionKeys::motifs
• duplicate_motif_cutoff : basic::options::OptionKeys::motifs
• dwell_cutoff : basic::options::OptionKeys::corrections::water
• dwkulp : basic::options::OptionKeys::dwkulp
• dx : 3d_histogram
• dy : 3d_histogram
• dyepos : basic::options::OptionKeys::AnchoredDesign::akash
• dynamic_grid_refinement : basic::options::OptionKeys::match
• dynamic_prof_calls : basic
• dynamic_prof_total : basic
• dz : 3d_histogram